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    JMJD1C jumonji domain containing 1C [ Homo sapiens (human) ]

    Gene ID: 221037, updated on 3-Mar-2024

    Summary

    Official Symbol
    JMJD1Cprovided by HGNC
    Official Full Name
    jumonji domain containing 1Cprovided by HGNC
    Primary source
    HGNC:HGNC:12313
    See related
    Ensembl:ENSG00000171988 MIM:604503; AllianceGenome:HGNC:12313
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KDM3C; TRIP8; TRIP-8
    Summary
    The protein encoded by this gene interacts with thyroid hormone receptors and contains a jumonji domain. It is a candidate histone demethylase and is thought to be a coactivator for key transcription factors. It plays a role in the DNA-damage response pathway by demethylating the mediator of DNA damage checkpoint 1 (MDC1) protein, and is required for the survival of acute myeloid leukemia. Mutations in this gene are associated with Rett syndrome and intellectual disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in bone marrow (RPKM 14.8), gall bladder (RPKM 12.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See JMJD1C in Genome Data Viewer
    Location:
    10q21.3
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (63167225..63521890, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (64025342..64380031, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (64926985..65281650, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3435 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:64940417-64940613 Neighboring gene nuclear receptor binding factor 2 Neighboring gene NANOG hESC enhancer GRCh37_chr10:64959364-64959900 Neighboring gene MPRA-validated peak963 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr10:65000486-65001022 Neighboring gene TatD DNase domain containing 1 pseudogene 1 Neighboring gene uncharacterized LOC124900287 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:65028313-65028838 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:65028839-65029362 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:65029678-65030178 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:65030179-65030679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3437 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:65120829-65121029 Neighboring gene NANOG hESC enhancer GRCh37_chr10:65125666-65126167 Neighboring gene microRNA 1296 Neighboring gene JMJD1C antisense RNA 2 Neighboring gene PRELID1 pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:65224969-65225758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3440 Neighboring gene JMJD1C antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3441 Neighboring gene receptor accessory protein 3 Neighboring gene Sharpr-MPRA regulatory region 5662 Neighboring gene uncharacterized LOC105378329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2410 Neighboring gene mitochondrial ribosomal protein L35 pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
    EBI GWAS Catalog
    A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation.
    EBI GWAS Catalog
    A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
    EBI GWAS Catalog
    A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.
    EBI GWAS Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genome-wide association analysis of juvenile idiopathic arthritis identifies a new susceptibility locus at chromosomal region 3q13.
    EBI GWAS Catalog
    Genome-wide association study identifies a new locus JMJD1C at 10q21 that may influence serum androgen levels in men.
    EBI GWAS Catalog
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    EBI GWAS Catalog
    Genome-wide association study indicates variants associated with insulin signaling and inflammation mediate lipoprotein responses to fenofibrate.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog
    Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists.
    EBI GWAS Catalog
    GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
    EBI GWAS Catalog
    Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
    EBI GWAS Catalog
    New gene functions in megakaryopoiesis and platelet formation.
    EBI GWAS Catalog
    Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ14374, KIAA1380, DKFZp761F0118

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K9 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9 demethylase activity TAS
    Traceable Author Statement
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclear thyroid hormone receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in blood coagulation TAS
    Traceable Author Statement
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    probable JmjC domain-containing histone demethylation protein 2C
    Names
    TR-interacting protein 8
    thyroid hormone receptor interactor 8
    thyroid receptor-interacting protein 8
    NP_001269877.1
    NP_001305082.1
    NP_001305083.1
    NP_001309181.1
    NP_001309183.1
    NP_001309187.1
    NP_116165.1
    XP_011537810.1
    XP_016871386.1
    XP_016871387.1
    XP_047280728.1
    XP_047280729.1
    XP_047280730.1
    XP_047280731.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_053187.2 RefSeqGene

      Range
      60913..359665
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001282948.2NP_001269877.1  probable JmjC domain-containing histone demethylation protein 2C isoform c

      See identical proteins and their annotated locations for NP_001269877.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as s-JMJD1C) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
      Source sequence(s)
      AL590502, AL607128, AL713895
      Consensus CDS
      CCDS60538.1
      UniProtKB/TrEMBL
      B7ZLC8
      Related
      ENSP00000444682.1, ENST00000542921.5
      Conserved Domains (3) summary
      smart00558
      Location:20962168
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam12067
      Location:546613
      Sox_C_TAD; Sox C-terminal transactivation domain
      cl21464
      Location:22002299
      cupin_like; Conserved domain found in cupin and related proteins
    2. NM_001318153.2NP_001305082.1  probable JmjC domain-containing histone demethylation protein 2C isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AL590502, AL607128, AL713895
      UniProtKB/TrEMBL
      B7ZLC8
      Conserved Domains (3) summary
      smart00558
      Location:19902062
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam12067
      Location:440507
      Sox_C_TAD; Sox C-terminal transactivation domain
      cl21464
      Location:20942193
      cupin_like; Conserved domain found in cupin and related proteins
    3. NM_001318154.2NP_001305083.1  probable JmjC domain-containing histone demethylation protein 2C isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as s-JMJD1C) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
      Source sequence(s)
      AC022022, AL590502, AL607128, AL713895
      Consensus CDS
      CCDS60538.1
      UniProtKB/TrEMBL
      B7ZLC8
      Conserved Domains (3) summary
      smart00558
      Location:20962168
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam12067
      Location:546613
      Sox_C_TAD; Sox C-terminal transactivation domain
      cl21464
      Location:22002299
      cupin_like; Conserved domain found in cupin and related proteins
    4. NM_001322252.2NP_001309181.1  probable JmjC domain-containing histone demethylation protein 2C isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (e) that is shorter than isoform a.
      Source sequence(s)
      AC022022, AL590502, AL713895
      UniProtKB/TrEMBL
      B7ZLC8
      Conserved Domains (3) summary
      smart00558
      Location:22402312
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam12067
      Location:690757
      Sox_C_TAD; Sox C-terminal transactivation domain
      cl21464
      Location:23442443
      cupin_like; Conserved domain found in cupin and related proteins
    5. NM_001322254.2NP_001309183.1  probable JmjC domain-containing histone demethylation protein 2C isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (f) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform f.
      Source sequence(s)
      AL590502, AL607128, AL713895
      UniProtKB/TrEMBL
      B7ZLC8
      Conserved Domains (3) summary
      smart00558
      Location:20592131
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:21632262
      cupin_like; Conserved domain found in cupin and related proteins
      cl26511
      Location:88453
      Neuromodulin_N; Gap junction protein N-terminal region
    6. NM_001322258.2NP_001309187.1  probable JmjC domain-containing histone demethylation protein 2C isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (f) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform f.
      Source sequence(s)
      AC022022, AL590502, AL607128, AL713895
      UniProtKB/TrEMBL
      B7ZLC8
      Conserved Domains (3) summary
      smart00558
      Location:20592131
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:21632262
      cupin_like; Conserved domain found in cupin and related proteins
      cl26511
      Location:88453
      Neuromodulin_N; Gap junction protein N-terminal region
    7. NM_032776.3NP_116165.1  probable JmjC domain-containing histone demethylation protein 2C isoform a

      See identical proteins and their annotated locations for NP_116165.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC022022, AL590502, AL607128, AL713895
      Consensus CDS
      CCDS41532.1
      UniProtKB/Swiss-Prot
      A0T124, Q15652, Q5SQZ8, Q5SQZ9, Q5SR00, Q7Z3E7, Q8N3U0, Q96KB9, Q9P2G7
      UniProtKB/TrEMBL
      B7ZLC8
      Related
      ENSP00000382204.2, ENST00000399262.7
      Conserved Domains (4) summary
      smart00558
      Location:22782350
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd14798
      Location:127175
      RX-CC_like; Coiled-coil domain of the potato virux X resistance protein and similar proteins
      pfam12067
      Location:728795
      Sox_C_TAD; Sox C-terminal transactivation domain
      cl21464
      Location:23822481
      cupin_like; Conserved domain found in cupin and related proteins

    RNA

    1. NR_134512.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains alternate 5' exon structure, lacks two internal exons, and uses two alternate splice sites, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, which is in-frame with the coding sequence of variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL590502, AL607128, AL713895
      Related
      ENST00000402544.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      63167225..63521890 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017015897.2XP_016871386.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

      UniProtKB/TrEMBL
      B7ZLC8
      Conserved Domains (3) summary
      smart00558
      Location:20962168
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam12067
      Location:546613
      Sox_C_TAD; Sox C-terminal transactivation domain
      cl21464
      Location:22002299
      cupin_like; Conserved domain found in cupin and related proteins
    2. XM_047424773.1XP_047280729.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

      UniProtKB/TrEMBL
      B7ZLC8
    3. XM_047424772.1XP_047280728.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

      UniProtKB/TrEMBL
      B7ZLC8
    4. XM_047424774.1XP_047280730.1  probable JmjC domain-containing histone demethylation protein 2C isoform X2

      UniProtKB/TrEMBL
      B7ZLC8
    5. XM_017015898.2XP_016871387.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

      UniProtKB/TrEMBL
      B7ZLC8
      Conserved Domains (3) summary
      smart00558
      Location:20962168
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam12067
      Location:546613
      Sox_C_TAD; Sox C-terminal transactivation domain
      cl21464
      Location:22002299
      cupin_like; Conserved domain found in cupin and related proteins
    6. XM_047424775.1XP_047280731.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

    7. XM_011539508.3XP_011537810.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      Conserved Domains (1) summary
      PTZ00121
      Location:125490
      PTZ00121; MAEBL; Provisional

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      64025342..64380031 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_004241.2: Suppressed sequence

      Description
      NM_004241.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.